@apollo-annotation/mst 0.3.5 → 0.3.6

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Files changed (14) hide show
  1. package/dist/AnnotationFeatureModel.d.ts +2 -1
  2. package/dist/AnnotationFeatureModel.js +40 -0
  3. package/dist/AnnotationFeatureModel.js.map +1 -1
  4. package/dist/ApolloAssembly.d.ts +8 -1
  5. package/dist/ApolloAssembly.js.map +1 -1
  6. package/dist/ApolloRefSeq.d.ts +3 -2
  7. package/dist/CheckResult.d.ts +2 -1
  8. package/dist/CheckResult.js.map +1 -1
  9. package/dist/tsconfig.tsbuildinfo +1 -1
  10. package/package.json +1 -1
  11. package/src/AnnotationFeatureModel.ts +47 -5
  12. package/src/ApolloAssembly.ts +1 -1
  13. package/src/ApolloRefSeq.ts +4 -4
  14. package/src/CheckResult.ts +1 -1
package/dist/AnnotationFeatureModel.d.ts CHANGED
@@ -1,4 +1,4 @@
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- import { IAnyModelType, IMSTMap, Instance, SnapshotIn, SnapshotOrInstance } from 'mobx-state-tree';
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+ import { type IAnyModelType, type IMSTMap, type Instance, type SnapshotIn, type SnapshotOrInstance } from 'mobx-state-tree';
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  export interface TranscriptPartLocation {
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  min: number;
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  max: number;
@@ -67,6 +67,7 @@ export declare const AnnotationFeatureModel: import("mobx-state-tree").IModelTyp
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  readonly transcriptParts: TranscriptParts[];
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  } & {
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  readonly cdsLocations: TranscriptPartCoding[][];
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+ readonly looksLikeGene: boolean;
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  } & {
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  setAttributes(attributes: Map<string, string[]>): void;
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  setAttribute(key: string, value: string[]): void;
package/dist/AnnotationFeatureModel.js CHANGED
@@ -240,6 +240,46 @@ exports.AnnotationFeatureModel = mobx_state_tree_1.types
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  const { transcriptParts } = self;
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  return transcriptParts.map((transcript) => transcript.filter((transcriptPart) => transcriptPart.type === 'CDS'));
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  },
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+ get looksLikeGene() {
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+ // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment, @typescript-eslint/no-explicit-any
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+ const session = (0, util_1.getSession)(self);
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+ // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment
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+ const { apolloDataStore } = session;
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+ // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment, @typescript-eslint/no-unsafe-member-access
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+ const { featureTypeOntology } = apolloDataStore.ontologyManager;
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+ if (!featureTypeOntology) {
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+ return false;
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+ }
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+ const children = self.children;
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+ if (!children?.size) {
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+ return false;
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+ }
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+ // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment
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+ const isGene =
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+ // eslint-disable-next-line @typescript-eslint/no-unsafe-call, @typescript-eslint/no-unsafe-member-access
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+ featureTypeOntology.isTypeOf(self.type, 'gene') ||
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+ // eslint-disable-next-line @typescript-eslint/no-unsafe-call, @typescript-eslint/no-unsafe-member-access
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+ featureTypeOntology.isTypeOf(self.type, 'pseudogene');
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+ if (!isGene) {
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+ return false;
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+ }
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+ for (const [, child] of children) {
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+ if (
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+ // eslint-disable-next-line @typescript-eslint/no-unsafe-call, @typescript-eslint/no-unsafe-member-access
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+ featureTypeOntology.isTypeOf(child.type, 'transcript') ||
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+ // eslint-disable-next-line @typescript-eslint/no-unsafe-call, @typescript-eslint/no-unsafe-member-access
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+ featureTypeOntology.isTypeOf(child.type, 'pseudogenic_transcript')) {
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+ const { children: grandChildren } = child;
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+ if (!grandChildren?.size) {
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+ return false;
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+ }
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+ return [...grandChildren.values()].some((grandchild) =>
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+ // eslint-disable-next-line @typescript-eslint/no-unsafe-call, @typescript-eslint/no-unsafe-member-access
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+ featureTypeOntology.isTypeOf(grandchild.type, 'exon'));
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+ }
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+ }
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+ return false;
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+ },
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  }))
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  .actions((self) => ({
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  setAttributes(attributes) {
package/dist/AnnotationFeatureModel.js.map CHANGED
@@ -1 +1 @@
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package/dist/ApolloAssembly.d.ts CHANGED
@@ -1,4 +1,4 @@
1
- import { Instance, SnapshotIn } from 'mobx-state-tree';
1
+ import { type Instance, type SnapshotIn } from 'mobx-state-tree';
2
2
  export type BackendDriverType = 'CollaborationServerDriver' | 'InMemoryFileDriver' | 'DesktopFileDriver';
3
3
  export declare const ApolloAssembly: import("mobx-state-tree").IModelType<{
4
4
  _id: import("mobx-state-tree").ISimpleType<string>;
@@ -25,6 +25,7 @@ export declare const ApolloAssembly: import("mobx-state-tree").IModelType<{
25
25
  readonly transcriptParts: import("./AnnotationFeatureModel").TranscriptPart[][];
26
26
  } & {
27
27
  readonly cdsLocations: import("./AnnotationFeatureModel").TranscriptPartCoding[][];
28
+ readonly looksLikeGene: boolean;
28
29
  } & {
29
30
  setAttributes(attributes: Map<string, string[]>): void;
30
31
  setAttribute(key: string, value: string[]): void;
@@ -87,6 +88,7 @@ export declare const ApolloAssembly: import("mobx-state-tree").IModelType<{
87
88
  readonly transcriptParts: import("./AnnotationFeatureModel").TranscriptPart[][];
88
89
  } & {
89
90
  readonly cdsLocations: import("./AnnotationFeatureModel").TranscriptPartCoding[][];
91
+ readonly looksLikeGene: boolean;
90
92
  } & {
91
93
  setAttributes(attributes: Map<string, string[]>): void;
92
94
  setAttribute(key: string, value: string[]): void;
@@ -128,6 +130,7 @@ export declare const ApolloAssembly: import("mobx-state-tree").IModelType<{
128
130
  readonly transcriptParts: import("./AnnotationFeatureModel").TranscriptPart[][];
129
131
  } & {
130
132
  readonly cdsLocations: import("./AnnotationFeatureModel").TranscriptPartCoding[][];
133
+ readonly looksLikeGene: boolean;
131
134
  } & {
132
135
  setAttributes(attributes: Map<string, string[]>): void;
133
136
  setAttribute(key: string, value: string[]): void;
@@ -190,6 +193,7 @@ export declare const ApolloAssembly: import("mobx-state-tree").IModelType<{
190
193
  readonly transcriptParts: import("./AnnotationFeatureModel").TranscriptPart[][];
191
194
  } & {
192
195
  readonly cdsLocations: import("./AnnotationFeatureModel").TranscriptPartCoding[][];
196
+ readonly looksLikeGene: boolean;
193
197
  } & {
194
198
  setAttributes(attributes: Map<string, string[]>): void;
195
199
  setAttribute(key: string, value: string[]): void;
@@ -250,6 +254,7 @@ export declare const ApolloAssembly: import("mobx-state-tree").IModelType<{
250
254
  readonly transcriptParts: import("./AnnotationFeatureModel").TranscriptPart[][];
251
255
  } & {
252
256
  readonly cdsLocations: import("./AnnotationFeatureModel").TranscriptPartCoding[][];
257
+ readonly looksLikeGene: boolean;
253
258
  } & {
254
259
  setAttributes(attributes: Map<string, string[]>): void;
255
260
  setAttribute(key: string, value: string[]): void;
@@ -291,6 +296,7 @@ export declare const ApolloAssembly: import("mobx-state-tree").IModelType<{
291
296
  readonly transcriptParts: import("./AnnotationFeatureModel").TranscriptPart[][];
292
297
  } & {
293
298
  readonly cdsLocations: import("./AnnotationFeatureModel").TranscriptPartCoding[][];
299
+ readonly looksLikeGene: boolean;
294
300
  } & {
295
301
  setAttributes(attributes: Map<string, string[]>): void;
296
302
  setAttribute(key: string, value: string[]): void;
@@ -353,6 +359,7 @@ export declare const ApolloAssembly: import("mobx-state-tree").IModelType<{
353
359
  readonly transcriptParts: import("./AnnotationFeatureModel").TranscriptPart[][];
354
360
  } & {
355
361
  readonly cdsLocations: import("./AnnotationFeatureModel").TranscriptPartCoding[][];
362
+ readonly looksLikeGene: boolean;
356
363
  } & {
357
364
  setAttributes(attributes: Map<string, string[]>): void;
358
365
  setAttribute(key: string, value: string[]): void;
package/dist/ApolloAssembly.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"ApolloAssembly.js","sourceRoot":"","sources":["../src/ApolloAssembly.ts"],"names":[],"mappings":";;;AAAA,qDAA6D;AAE7D,iDAA6C;AAOhC,QAAA,cAAc,GAAG,uBAAK;KAChC,KAAK,CAAC,gBAAgB,EAAE;IACvB,GAAG,EAAE,uBAAK,CAAC,UAAU;IACrB,OAAO,EAAE,uBAAK,CAAC,GAAG,CAAC,2BAAY,CAAC;IAChC,QAAQ,EAAE,uBAAK,CAAC,KAAK,CAAC,uBAAK,CAAC,MAAM,CAAC;IACnC,iBAAiB,EAAE,uBAAK,CAAC,QAAQ,CAC/B,uBAAK,CAAC,WAAW,CAAC,mBAAmB,EAAE;QACrC,2BAA2B;QAC3B,oBAAoB;QACpB,mBAAmB;KACpB,CAAC,EACF,2BAA2B,CAC5B;CACF,CAAC;KACD,KAAK,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC;IAChB,YAAY,CAAC,OAAe;QAC1B,OAAO,CAAC,GAAG,IAAI,CAAC,OAAO,CAAC,MAAM,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,EAAE,EAAE,CAAC,GAAG,CAAC,IAAI,KAAK,OAAO,CAAC,CAAA;IACvE,CAAC;CACF,CAAC,CAAC;KACF,OAAO,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC;IAClB,SAAS,CAAC,EAAU,EAAE,IAAY,EAAE,WAAoB;QACtD,OAAO,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE,GAAG,EAAE,EAAE,EAAE,IAAI,EAAE,WAAW,EAAE,CAAC,CAAA;IACzD,CAAC;IACD,UAAU,CAAC,OAAe;QACxB,OAAO,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;IACpC,CAAC;CACF,CAAC,CAAC,CAAA"}
1
+ {"version":3,"file":"ApolloAssembly.js","sourceRoot":"","sources":["../src/ApolloAssembly.ts"],"names":[],"mappings":";;;AAAA,qDAAuE;AAEvE,iDAA6C;AAOhC,QAAA,cAAc,GAAG,uBAAK;KAChC,KAAK,CAAC,gBAAgB,EAAE;IACvB,GAAG,EAAE,uBAAK,CAAC,UAAU;IACrB,OAAO,EAAE,uBAAK,CAAC,GAAG,CAAC,2BAAY,CAAC;IAChC,QAAQ,EAAE,uBAAK,CAAC,KAAK,CAAC,uBAAK,CAAC,MAAM,CAAC;IACnC,iBAAiB,EAAE,uBAAK,CAAC,QAAQ,CAC/B,uBAAK,CAAC,WAAW,CAAC,mBAAmB,EAAE;QACrC,2BAA2B;QAC3B,oBAAoB;QACpB,mBAAmB;KACpB,CAAC,EACF,2BAA2B,CAC5B;CACF,CAAC;KACD,KAAK,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC;IAChB,YAAY,CAAC,OAAe;QAC1B,OAAO,CAAC,GAAG,IAAI,CAAC,OAAO,CAAC,MAAM,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,EAAE,EAAE,CAAC,GAAG,CAAC,IAAI,KAAK,OAAO,CAAC,CAAA;IACvE,CAAC;CACF,CAAC,CAAC;KACF,OAAO,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC;IAClB,SAAS,CAAC,EAAU,EAAE,IAAY,EAAE,WAAoB;QACtD,OAAO,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE,GAAG,EAAE,EAAE,EAAE,IAAI,EAAE,WAAW,EAAE,CAAC,CAAA;IACzD,CAAC;IACD,UAAU,CAAC,OAAe;QACxB,OAAO,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;IACpC,CAAC;CACF,CAAC,CAAC,CAAA"}
package/dist/ApolloRefSeq.d.ts CHANGED
@@ -1,5 +1,5 @@
1
- import { Instance, SnapshotIn, SnapshotOrInstance } from 'mobx-state-tree';
2
- import { AnnotationFeatureSnapshot } from './AnnotationFeatureModel';
1
+ import { type Instance, type SnapshotIn, type SnapshotOrInstance } from 'mobx-state-tree';
2
+ import { type AnnotationFeatureSnapshot } from './AnnotationFeatureModel';
3
3
  export declare const Sequence: import("mobx-state-tree").IModelType<{
4
4
  start: import("mobx-state-tree").ISimpleType<number>;
5
5
  stop: import("mobx-state-tree").ISimpleType<number>;
@@ -28,6 +28,7 @@ export declare const ApolloRefSeq: import("mobx-state-tree").IModelType<{
28
28
  readonly transcriptParts: import("./AnnotationFeatureModel").TranscriptPart[][];
29
29
  } & {
30
30
  readonly cdsLocations: import("./AnnotationFeatureModel").TranscriptPartCoding[][];
31
+ readonly looksLikeGene: boolean;
31
32
  } & {
32
33
  setAttributes(attributes: Map<string, string[]>): void;
33
34
  setAttribute(key: string, value: string[]): void;
package/dist/CheckResult.d.ts CHANGED
@@ -1,4 +1,4 @@
1
- import { Instance, SnapshotIn } from 'mobx-state-tree';
1
+ import { type Instance, type SnapshotIn } from 'mobx-state-tree';
2
2
  export declare const CheckResult: import("mobx-state-tree").IModelType<{
3
3
  _id: import("mobx-state-tree").ISimpleType<string>;
4
4
  name: import("mobx-state-tree").ISimpleType<string>;
@@ -22,6 +22,7 @@ export declare const CheckResult: import("mobx-state-tree").IModelType<{
22
22
  readonly transcriptParts: import("./AnnotationFeatureModel").TranscriptPart[][];
23
23
  } & {
24
24
  readonly cdsLocations: import("./AnnotationFeatureModel").TranscriptPartCoding[][];
25
+ readonly looksLikeGene: boolean;
25
26
  } & {
26
27
  setAttributes(attributes: Map<string, string[]>): void;
27
28
  setAttribute(key: string, value: string[]): void;
package/dist/CheckResult.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"CheckResult.js","sourceRoot":"","sources":["../src/CheckResult.ts"],"names":[],"mappings":";;;AAAA,qDAA6D;AAE7D,qEAAiE;AAEpD,QAAA,WAAW,GAAG,uBAAK,CAAC,KAAK,CAAC,aAAa,EAAE;IACpD,GAAG,EAAE,uBAAK,CAAC,UAAU;IACrB,IAAI,EAAE,uBAAK,CAAC,MAAM;IAClB,KAAK,EAAE,uBAAK,CAAC,MAAM;IACnB,GAAG,EAAE,uBAAK,CAAC,KAAK,CAAC,uBAAK,CAAC,aAAa,CAAC,+CAAsB,CAAC,CAAC;IAC7D,MAAM,EAAE,uBAAK,CAAC,MAAM;IACpB,KAAK,EAAE,uBAAK,CAAC,MAAM;IACnB,GAAG,EAAE,uBAAK,CAAC,MAAM;IACjB,OAAO,EAAE,KAAK;IACd,OAAO,EAAE,uBAAK,CAAC,MAAM;CACtB,CAAC,CAAA"}
1
+ {"version":3,"file":"CheckResult.js","sourceRoot":"","sources":["../src/CheckResult.ts"],"names":[],"mappings":";;;AAAA,qDAAuE;AAEvE,qEAAiE;AAEpD,QAAA,WAAW,GAAG,uBAAK,CAAC,KAAK,CAAC,aAAa,EAAE;IACpD,GAAG,EAAE,uBAAK,CAAC,UAAU;IACrB,IAAI,EAAE,uBAAK,CAAC,MAAM;IAClB,KAAK,EAAE,uBAAK,CAAC,MAAM;IACnB,GAAG,EAAE,uBAAK,CAAC,KAAK,CAAC,uBAAK,CAAC,aAAa,CAAC,+CAAsB,CAAC,CAAC;IAC7D,MAAM,EAAE,uBAAK,CAAC,MAAM;IACpB,KAAK,EAAE,uBAAK,CAAC,MAAM;IACnB,GAAG,EAAE,uBAAK,CAAC,MAAM;IACjB,OAAO,EAAE,KAAK;IACd,OAAO,EAAE,uBAAK,CAAC,MAAM;CACtB,CAAC,CAAA"}